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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MSPrep.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MSPrep_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MSPrep.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSPrep/DESCRIPTION’ ... OK
* this is package ‘MSPrep’ version ‘1.20.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSPrep’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MSPrep      18.631  0.435  19.068
msImpute    17.447  0.359  17.807
msNormalize 13.476  0.127  13.605
msPrepare   13.186  0.110  13.297
msSummarize 12.431  0.086  12.518
msFilter    12.272  0.097  12.369
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │ └─dplyr:::summarise.data.frame(.tbl, !!!funs)
    4. │   └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
    5. │     └─base::withCallingHandlers(...)
    6. ├─dplyr:::dplyr_internal_error(...)
    7. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
    8. │   └─rlang:::signal_abort(cnd, .file)
    9. │     └─base::signalCondition(cnd)
   10. └─dplyr (local) `<fn>`(`<dpl:::__>`)
   11.   └─dplyr (local) handler(cnd)
   12.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 11 | SKIP 0 | PASS 78 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MSPrep.Rcheck/00check.log’
for details.